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GEMINI windower (version 0.20.1)

GEMINI database:

Only files with version 0.20.1 are accepted.

The type of window analysis requested?:

The operation that should be applied to the -t values:

Window size in bp:

Step size for sliding the window in bp:

Specify 0 here for sliding by one full window size

What it does

Compute variation metrics across genomic windows.

Examples

Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows:

-w 50000
-s 0
-t nucl_div
-o mean

Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 40kb:

-w 50000
-s 10000
-t nucl_div
-o mean

Compute the max value for HWE statistics for all variants in 10kb windows every 100kb along the genome:

-w 10000
-s 100000
-t hwe
-o max